[English] 日本語
Yorodumi
- PDB-3q9x: Crystal structure of human CK2 alpha in complex with emodin at pH 6.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q9x
TitleCrystal structure of human CK2 alpha in complex with emodin at pH 6.5
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-7PE / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / DI(HYDROXYETHYL)ETHER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBattistutta, R. / Ranchio, A. / Papinutto, E.
CitationJournal: To be Published
Title: Structural and functional analysis of the flexible regions of the catalytic alpha-subunit of protein kinase CK2
Authors: Papinutto, E. / Ranchio, A. / Lolli, G. / Pinna, L.A. / Battistutta, R.
History
DepositionJan 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,06115
Polymers80,3082
Non-polymers1,75413
Water4,450247
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0857
Polymers40,1541
Non-polymers9316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9768
Polymers40,1541
Non-polymers8237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.010, 128.010, 124.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA4 - 314 - 31
21PROPROVALVALBB4 - 314 - 31
12TRPTRPILEILEAA33 - 10033 - 100
22TRPTRPILEILEBB33 - 10033 - 100
13THRTHRPROPROAA129 - 159129 - 159
23THRTHRPROPROBB129 - 159129 - 159
14ASNASNILEILEAA161 - 174161 - 174
24ASNASNILEILEBB161 - 174161 - 174
15TRPTRPLYSLYSAA176 - 229176 - 229
25TRPTRPLYSLYSBB176 - 229176 - 229
16GLNGLNLYSLYSAA241 - 329241 - 329
26GLNGLNLYSLYSBB241 - 329241 - 329

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK2alpha / CK II alpha


Mass: 40153.820 Da / Num. of mol.: 2 / Fragment: UNP residues 1-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68400, non-specific serine/threonine protein kinase

-
Non-polymers , 6 types, 260 molecules

#2: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN / Emodin


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972937 Å / Relative weight: 1
ReflectionResolution: 2.2→73.32 Å / Num. all: 44592 / Num. obs: 44592 / % possible obs: 85.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3220.7570.5830.91286464990.4770.7570.5831.786.4
2.32-2.462.30.5090.4051.71462864570.3040.5090.4052.690.3
2.46-2.632.30.3550.2842.51371060130.210.3550.2843.789.4
2.63-2.842.30.2340.1873.31278255270.1380.2340.1875.488.1
2.84-3.112.30.1420.1146.21173050040.0830.1420.114886.4
3.11-3.482.40.0920.0748.81061344510.0530.0920.07411.484.9
3.48-4.022.40.0670.0549.7928738350.0380.0670.05415.482.4
4.02-4.922.50.0560.04611.8776831460.0320.0560.04618.579.6
4.92-6.962.40.050.04113.3564523400.0280.050.04119.275.9
6.96-73.3242.60.0460.03710.4341713200.0270.0460.03723.474.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ProDCdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVR

2pvr


Resolution: 2.2→73.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2337 / WRfactor Rwork: 0.1941 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8518 / SU B: 11.24 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2619 / SU Rfree: 0.2166 / Cross valid method: THROUGHOUT / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 2294 5.1 %RANDOM
Rwork0.1941 ---
obs0.1966 44560 84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98 Å2 / Biso mean: 34.194 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0 Å2
2--0.39 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 111 247 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0215858
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9637925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.089314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.727151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9581551
X-RAY DIFFRACTIONr_chiral_restr0.1410.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214503
X-RAY DIFFRACTIONr_mcbond_it0.8981.53313
X-RAY DIFFRACTIONr_mcangle_it1.64925391
X-RAY DIFFRACTIONr_scbond_it2.88532545
X-RAY DIFFRACTIONr_scangle_it4.5564.52533
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1128TIGHT POSITIONAL0.080.05
1261MEDIUM POSITIONAL0.210.5
1128TIGHT THERMAL0.230.5
1261MEDIUM THERMAL0.282
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 163 -
Rwork0.291 2977 -
all-3140 -
obs--81.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2202-0.3281-0.02310.8718-0.00011.04460.03020.15060.1399-0.0289-0.0417-0.0282-0.08680.0190.01140.1167-0.017300.07470.00160.08386.364845.6284.451
22.0976-0.0674-1.34051.7275-0.94723.68470.008-0.12-0.01890.0242-0.0166-0.0199-0.04680.05610.00850.18120.037-0.00760.1224-0.01380.1654-10.720552.316222.2146
31.78620.1382-0.12090.1917-0.42951.7640.0251-0.01620.19960.00360.00390.0976-0.1968-0.1829-0.0290.1072-0.0042-0.02490.1247-0.01610.121-6.174249.100613.8651
40.6406-0.51661.06030.9087-1.35612.68550.0486-0.311-0.16820.15740.0851-0.01770.1565-0.2097-0.13360.2755-0.0221-0.03790.28790.05860.2286-3.654540.569831.3921
50.98430.20.14581.7879-0.75940.84930.0152-0.2356-0.05210.27650.02190.20080.004-0.1861-0.03710.1054-0.00740.00630.1042-0.01620.1094.224234.99924.7379
61.1528-0.34190.44620.63560.11811.7920.0103-0.15620.05960.1405-0.02060.0036-0.10290.05970.01040.10840.00860.00340.0876-0.00830.118813.517144.797623.1888
71.46180.2415-0.13441.4043-0.26622.01050.0399-0.07960.10660.102-0.0424-0.0346-0.11220.12270.00240.10750.0519-0.00060.1267-0.00840.133622.422536.361527.3169
88.8422-6.4562-2.11478.80812.73012.01430.19580.3836-0.0326-0.2822-0.2575-0.34990.29380.33620.06170.27220.03060.03050.28560.02670.2206-17.802936.0562-21.5614
90.9970.56050.25561.53710.95711.23690.0066-0.04760.0633-0.00070.0443-0.1605-0.10820.1613-0.05090.09610.01350.00030.09850.02890.0918-14.881868.2136-14.9317
100.2540.1124-0.10170.13640.05520.15660.0039-0.2497-0.25820.1836-0.1047-0.11550.20870.10770.10080.38190.0031-0.00170.3880.11660.395-26.483964.94192.4182
111.9407-0.2488-0.71790.7847-0.18130.85480.0222-0.25410.21990.19590.01820.0645-0.1964-0.0366-0.04050.10450.0027-0.01450.1037-0.0090.1061-30.0758.2095-6.6057
120.63460.51350.23021.5146-0.1911.9918-0.0185-0.09390.01180.10240.0198-0.06990.05350.0842-0.00130.0833-0.0143-0.00740.11180.00540.1073-19.684350.3292-10.7156
132.6173-0.8025-0.10140.9741-0.27930.7961-0.0408-0.1710.11510.1510.0848-0.17070.01120.1253-0.04410.1516-0.01160.00270.14440.01980.1291-21.617840.27591.6674
141.4772-0.1576-0.38421.33980.11742.011-0.0453-0.1145-0.02930.08870.0418-0.07170.08890.05550.00350.1289-0.0541-0.01080.0984-0.00640.1299-30.36941.4535-2.9725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 36
2X-RAY DIFFRACTION2A37 - 77
3X-RAY DIFFRACTION3A78 - 112
4X-RAY DIFFRACTION4A113 - 125
5X-RAY DIFFRACTION5A126 - 167
6X-RAY DIFFRACTION6A168 - 243
7X-RAY DIFFRACTION7A244 - 331
8X-RAY DIFFRACTION8B2 - 9
9X-RAY DIFFRACTION9B10 - 113
10X-RAY DIFFRACTION10B114 - 127
11X-RAY DIFFRACTION11B128 - 167
12X-RAY DIFFRACTION12B168 - 221
13X-RAY DIFFRACTION13B222 - 258
14X-RAY DIFFRACTION14B259 - 331

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more